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<div class="header">
  <div class="summary">
<a href="#pub-types">Public Types</a> &#124;
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
<a href="#pub-attribs">Public Attributes</a> &#124;
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<p><code>#include &lt;<a class="el" href="_distance_calculator_8hpp_source.html">DistanceCalculator.hpp</a>&gt;</code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:affde42ac598a1597aba092e781de6609"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609">CorrectionType</a> { <br />
&#160;&#160;<a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609a5f3b3cb6619f0d29daf2ff29a772d93c">not_assigned</a>, 
<a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609a4f1b606366478e0f0f4c8acd4de71583">none</a>, 
<a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609aeb17fea69ad9aef888f2419a2814abf9">JukesCantor</a>, 
<a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609a08d9cb898efb2c44ad9fd7b09d6c7e50">Kimura2</a>, 
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&#160;&#160;<a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609a82d5f2ef688449e3584c82448b739b88">FastTree</a>
<br />
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<tr class="memitem:aba37861b27b2e9a8e12b0aea4fcb5c7c"><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7c">AlphabetType</a> { <a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7cafb040d095728a3f8116779a3cd63b2af">dna</a>, 
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<a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7ca36b2c09e572187e6f03fa8bde6fda574">null</a>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a2a8861e559827f4a9324b854edc13e58"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a2a8861e559827f4a9324b854edc13e58">DistanceCalculator</a> (std::string **<a class="el" href="class_distance_calculator.html#a00bdfa4cc790ce19056cf06894e205f4">A</a>, <a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7c">AlphabetType</a> alphType, <a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609">CorrectionType</a> corrType, int <a class="el" href="class_distance_calculator.html#a0a797aedff55422df2d8dc526d397bcb">numberOfSequences</a>, bool useSSE)</td></tr>
<tr class="separator:a2a8861e559827f4a9324b854edc13e58"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a937924271f1403a83408b4807589bd91"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a937924271f1403a83408b4807589bd91">~DistanceCalculator</a> ()</td></tr>
<tr class="separator:a937924271f1403a83408b4807589bd91"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3103ea39f1b1dbdbb7e23afd2adbd959"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a3103ea39f1b1dbdbb7e23afd2adbd959">calc</a> (int a, int b)</td></tr>
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<tr class="memitem:ac315efce21a47f3e77fb61ea933f930b"><td class="memItemLeft" align="right" valign="top">double&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#ac315efce21a47f3e77fb61ea933f930b">testDifferenceCluster</a> (int a, int b)</td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:a852203aaa2f7eb7faf53cc52245244f1"><td class="memItemLeft" align="right" valign="top">static int *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a852203aaa2f7eb7faf53cc52245244f1">getInverseAlphabet</a> (std::string alph, int length)</td></tr>
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Public Attributes</h2></td></tr>
<tr class="memitem:a7d15fa02f8da2455998c97b3c18d0bc0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7c">AlphabetType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a7d15fa02f8da2455998c97b3c18d0bc0">alph_type</a></td></tr>
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<tr class="memitem:a546dee19652efa8267f27b4baead4dfb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609">CorrectionType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a546dee19652efa8267f27b4baead4dfb">corr_type</a></td></tr>
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<tr class="memitem:a1f57ec0ac50ea709a7a8c349167d6199"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a1f57ec0ac50ea709a7a8c349167d6199">dna_chars</a></td></tr>
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<tr class="memitem:a721cb1b004a4d856515be5b8c4fc0fc4"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a721cb1b004a4d856515be5b8c4fc0fc4">aa_chars</a></td></tr>
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<tr class="memitem:a00bdfa4cc790ce19056cf06894e205f4"><td class="memItemLeft" align="right" valign="top">std::string **&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a00bdfa4cc790ce19056cf06894e205f4">A</a></td></tr>
<tr class="separator:a00bdfa4cc790ce19056cf06894e205f4"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0a797aedff55422df2d8dc526d397bcb"><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a0a797aedff55422df2d8dc526d397bcb">numberOfSequences</a></td></tr>
<tr class="separator:a0a797aedff55422df2d8dc526d397bcb"><td class="memSeparator" colspan="2">&#160;</td></tr>
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<tr class="memitem:aab6b17cfa53aa960ed4fcfadfb160408"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#aab6b17cfa53aa960ed4fcfadfb160408">newCalculation</a></td></tr>
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<tr class="memitem:a99279654c09ff392eed4cf5b03051158"><td class="memItemLeft" align="right" valign="top">unsigned int **&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a99279654c09ff392eed4cf5b03051158">convertedSequences</a></td></tr>
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<tr class="memitem:ae6a08d5f607d2fab97983f956dcee6eb"><td class="memItemLeft" align="right" valign="top">unsigned int **&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#ae6a08d5f607d2fab97983f956dcee6eb">gapInTheSequences</a></td></tr>
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<tr class="memitem:a61a73417e46e0c2b9a4d5d95a6ed4d81"><td class="memItemLeft" align="right" valign="top">__m128i&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_distance_calculator.html#a61a73417e46e0c2b9a4d5d95a6ed4d81">x128</a></td></tr>
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<h2 class="groupheader">Member Enumeration Documentation</h2>
<a id="aba37861b27b2e9a8e12b0aea4fcb5c7c"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aba37861b27b2e9a8e12b0aea4fcb5c7c">&#9670;&nbsp;</a></span>AlphabetType</h2>

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          <td class="memname">enum <a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7c">DistanceCalculator::AlphabetType</a></td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="aba37861b27b2e9a8e12b0aea4fcb5c7cafb040d095728a3f8116779a3cd63b2af"></a>dna&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="aba37861b27b2e9a8e12b0aea4fcb5c7cad0f2f6fb9391cbe99f3f7b9dc4cfd63a"></a>amino&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="aba37861b27b2e9a8e12b0aea4fcb5c7ca36b2c09e572187e6f03fa8bde6fda574"></a>null&#160;</td><td class="fielddoc"></td></tr>
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<h2 class="memtitle"><span class="permalink"><a href="#affde42ac598a1597aba092e781de6609">&#9670;&nbsp;</a></span>CorrectionType</h2>

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<tr><td class="fieldname"><a id="affde42ac598a1597aba092e781de6609a4f1b606366478e0f0f4c8acd4de71583"></a>none&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="affde42ac598a1597aba092e781de6609aeb17fea69ad9aef888f2419a2814abf9"></a>JukesCantor&#160;</td><td class="fielddoc"></td></tr>
<tr><td class="fieldname"><a id="affde42ac598a1597aba092e781de6609a08d9cb898efb2c44ad9fd7b09d6c7e50"></a>Kimura2&#160;</td><td class="fielddoc"></td></tr>
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<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a2a8861e559827f4a9324b854edc13e58">&#9670;&nbsp;</a></span>DistanceCalculator()</h2>

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          <td></td>
          <td class="paramtype"><a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609">CorrectionType</a>&#160;</td>
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<h2 class="memtitle"><span class="permalink"><a href="#a937924271f1403a83408b4807589bd91">&#9670;&nbsp;</a></span>~DistanceCalculator()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a3103ea39f1b1dbdbb7e23afd2adbd959">&#9670;&nbsp;</a></span>calc()</h2>

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          <td class="memname">double DistanceCalculator::calc </td>
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<h2 class="memtitle"><span class="permalink"><a href="#a852203aaa2f7eb7faf53cc52245244f1">&#9670;&nbsp;</a></span>getInverseAlphabet()</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#ac315efce21a47f3e77fb61ea933f930b">&#9670;&nbsp;</a></span>testDifferenceCluster()</h2>

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<h2 class="groupheader">Member Data Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a00bdfa4cc790ce19056cf06894e205f4">&#9670;&nbsp;</a></span>A</h2>

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          <td class="memname"><a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7c">AlphabetType</a> DistanceCalculator::alph_type</td>
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          <td class="memname"><a class="el" href="class_distance_calculator.html#affde42ac598a1597aba092e781de6609">CorrectionType</a> DistanceCalculator::corr_type</td>
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<h2 class="memtitle"><span class="permalink"><a href="#ab530628f3fb6f7e216ef6d378665e66a">&#9670;&nbsp;</a></span>COUNTS_MASK</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a9f70a25047b64665cb1ac392482df94f">&#9670;&nbsp;</a></span>DECOMPRESSED_GAPS</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a1f57ec0ac50ea709a7a8c349167d6199">&#9670;&nbsp;</a></span>dna_chars</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#aab6b17cfa53aa960ed4fcfadfb160408">&#9670;&nbsp;</a></span>newCalculation</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a0a797aedff55422df2d8dc526d397bcb">&#9670;&nbsp;</a></span>numberOfSequences</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a47d1216e0b5d0cbc662a7c151d283329">&#9670;&nbsp;</a></span>TRANSITIONS_MASK</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#ab1a3b734787d672be007ec68c1b48cd7">&#9670;&nbsp;</a></span>TRANSVERSIONS_MASK</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a68fa9153f40a2a4b67afb724eb8264aa">&#9670;&nbsp;</a></span>VALUES_0</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#a61a73417e46e0c2b9a4d5d95a6ed4d81">&#9670;&nbsp;</a></span>x128</h2>

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<h2 class="memtitle"><span class="permalink"><a href="#aa6b5621fcd3799f2b7e5840c75015c25">&#9670;&nbsp;</a></span>zero</h2>

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<hr/>The documentation for this class was generated from the following files:<ul>
<li>NINJA/<a class="el" href="_distance_calculator_8hpp_source.html">DistanceCalculator.hpp</a></li>
<li>NINJA/<a class="el" href="_distance_calculator_8cpp.html">DistanceCalculator.cpp</a></li>
</ul>
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